Pressure or flow is the only way to do this, speed would get you all fouled up. It should work, each loop will be looking at the pipe pressure and regardless of what the other VFD is doing, each one should be reacting ONLY to the situation in the pipe. If you think it through a bit, what's the difference between that and having a varying input pressure on the pipe and having one pump trying to deal with that with a PID loop? So if you substitute a natural variation situation with one produced by another pump in the system, what's the difference?
But tuning the two PID loops would be a bit of a PITA. No two pumps, and the wells they are in, and the pipes they feed into are going to be exactly the same. So you are going to have to tweak the slew rates on the PID loops, most likely by messing with the accel / decel rates on the VFDs in accordance with the differences in water table, pump set depth, pipe friction etc. I wouldn't want to be the guy to do this, these kinds of things never go well for me.
So a word to the wise:
Don't use the PID capability inside the VFDs. I know most of them have it built-in now, but here's my reasoning, and it ESPECIALLY applies to a PITA situation like this. The problem is, if the VFD dies and has to be replaced, you loose the PID programming in it and have to do it ALL OVER AGAIN! Whereas if you use a separate PLC or even a name brand loop controller, if the VFD dies, all you have to do is match the basic programming of the drives. All the complicated stuff for the PID loop tuning stays behind and doesn't change. It's a BIG pitfall people fell in to when VFD mfrs sought to "simplify" installations by integrating PI or PID control into the VFDs. The hidden "gotcha" is that unless you are willing to go through all of the tuning again, the only way to recover from a disaster or drive failure is to buy an IDENTICAL replacement drive from them, you can't go out and buy the fastest one available ! Then if, as is usually the case now, the original one has been replaced and no longer available, you are screwed.
Been there, done that, got the t-shirt and the hat.